plotGenes: Plot genes

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Plot genes

Description

Plot genes in a window of interest.

Usage

plotGenes(
  window,
  TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene,
  longest = TRUE,
  xlim = NULL,
  font_size = 14
)

Arguments

window	GRanges object with coordinates to use for selecting the genes to plot.
TxDb	TxDb object to use for drawing the genomic annotation.
longest	Logical indicating whether to plot only the longest transcripts for each gene in the gene annotation plot.
xlim	Limits for the plot x axis (genomic coordinates).
font_size	Base font size to use for the UMI4C plot. Default: 14.

Value

Produces a plot with the genes found in the provided window.

Examples

window <- GRanges("chr16:11348649-11349648")
plotGenes(
    window = window,
    TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
)

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.